libSBML Python API
5.10.0
|
{core}
Log of errors and other events encountered during SBML processing.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The error log is a list. Each SBMLDocument maintains its own SBMLErrorLog. When a libSBML operation on SBML content results in an error, or when there is something worth noting about the SBML content, the issue is reported as an SBMLError object stored in the SBMLErrorLog list.
SBMLErrorLog is derived from XMLErrorLog, an object class that serves exactly the same purpose but for the XML parsing layer. XMLErrorLog provides crucial methods such as getNumErrors() for determining how many SBMLError or XMLError objects are in the log. SBMLErrorLog inherits these methods.
The general approach to working with SBMLErrorLog in user programs involves first obtaining a pointer to a log from a libSBML object such as SBMLDocument. Callers should then use getNumErrors() to inquire how many objects there are in the list. (The answer may be 0.) If there is at least one SBMLError object in the SBMLErrorLog instance, callers can then iterate over the list using SBMLErrorLog.getError(), using methods provided by the SBMLError class to find out the error code and associated information such as the error severity, the message, and the line number in the input.
If you wish to simply print the error strings for a human to read, an easier and more direct way might be to use SBMLDocument.printErrors().
Public Member Functions | |
def | add |
def | changeErrorSeverity |
def | clearLog |
def | contains |
def | getError |
def | getNumErrors |
def | getNumFailsWithSeverity |
def | getSeverityOverride |
def | isSeverityOverridden |
def | printErrors |
def | remove |
def | setSeverityOverride |
def | toString |
def | unsetSeverityOverride |
def libsbml.SBMLErrorLog.add | ( | self, | |
args | |||
) |
Python method signature(s):
add(SBMLErrorLog self, SBMLError error)
|
inherited |
Python method signature(s):
changeErrorSeverity(XMLErrorLog self, long originalSeverity, long targetSeverity, string package="all") changeErrorSeverity(XMLErrorLog self, long originalSeverity, long targetSeverity)
Changes the severity override for errors in the log that have a given severity.
This searches through the list of errors in the log, comparing each one's severity to the value of originalSeverity
. For each error encountered with that severity logged by the named package
, the severity of the error is reset to targetSeverity
.
originalSeverity | the severity code to match |
targetSeverity | the severity code to use as the new severity |
package | a string, the name of an SBML Level 3 package extension to use to narrow the search for errors. A value of 'all' signifies to match against errors logged from any package; a value of a package nickname such as 'comp' signifies to limit consideration to errors from just that package. |
|
inherited |
def libsbml.SBMLErrorLog.contains | ( | self, | |
args | |||
) |
Python method signature(s):
contains(SBMLErrorLog self, long errorId)bool
Returns true if SBMLErrorLog contains an errorId
errorId | the error identifier of the error to be found. |
def libsbml.SBMLErrorLog.getError | ( | self, | |
args | |||
) |
{core}
Log of errors and other events encountered during SBML processing.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The error log is a list. Each SBMLDocument maintains its own SBMLErrorLog. When a libSBML operation on SBML content results in an error, or when there is something worth noting about the SBML content, the issue is reported as an SBMLError object stored in the SBMLErrorLog list.
SBMLErrorLog is derived from XMLErrorLog, an object class that serves exactly the same purpose but for the XML parsing layer. XMLErrorLog provides crucial methods such as getNumErrors() for determining how many SBMLError or XMLError objects are in the log. SBMLErrorLog inherits these methods.
The general approach to working with SBMLErrorLog in user programs involves first obtaining a pointer to a log from a libSBML object such as SBMLDocument. Callers should then use getNumErrors() to inquire how many objects there are in the list. (The answer may be 0.) If there is at least one SBMLError object in the SBMLErrorLog instance, callers can then iterate over the list using SBMLErrorLog.getError(), using methods provided by the SBMLError class to find out the error code and associated information such as the error severity, the message, and the line number in the input.
If you wish to simply print the error strings for a human to read, an easier and more direct way might be to use SBMLDocument.printErrors().
getError(SBMLErrorLog self, long n)SBMLError
Returns the nth SBMLError object in this log.
Index n
is counted from 0. Callers should first inquire about the number of items in the log by using the getNumErrors() method. Attempts to use an error index number that exceeds the actual number of errors in the log will result in a None
being returned.
n | the index number of the error to retrieve (with 0 being the first error). |
None
if n
is greater than or equal to getNumErrors().
|
inherited |
{core}
Log of errors and other events encountered while processing an XML file or data stream.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The error log is a list. The XML layer of libSBML maintains an error log associated with a given XML document or data stream. When an operation results in an error, or when there is something wrong with the XML content, the problem is reported as an XMLError object stored in the XMLErrorLog list. Potential problems range from low-level issues (such as the inability to open a file) to XML syntax errors (such as mismatched tags or other problems).
A typical approach for using this error log is to first use getNumErrors() to inquire how many XMLError object instances it contains, and then to iterate over the list of objects one at a time using getError(long n) const. Indexing in the list begins at 0.
In normal circumstances, programs using libSBML will actually obtain an SBMLErrorLog rather than an XMLErrorLog. The former is subclassed from XMLErrorLog and simply wraps commands for working with SBMLError objects rather than the low-level XMLError objects. Classes such as SBMLDocument use the higher-level SBMLErrorLog. Python method signature(s):
getNumErrors(XMLErrorLog self)long
Returns the number of errors that have been logged.
To retrieve individual errors from the log, callers may use XMLErrorLog.getError() .
def libsbml.SBMLErrorLog.getNumFailsWithSeverity | ( | self, | |
args | |||
) |
Python method signature(s):
getNumFailsWithSeverity(SBMLErrorLog self, long severity)long getNumFailsWithSeverity(SBMLErrorLog self, long severity)
long
Returns the number of errors that have been logged with the given severity code.
severity | a value from the set of LIBSBML_SEV_ constants defined by the interface class libsbml. |
|
inherited |
Python method signature(s):
getSeverityOverride(XMLErrorLog self)long
Returns the current override.
|
inherited |
Python method signature(s):
isSeverityOverridden(XMLErrorLog self)bool
Returns a boolean indicating whether or not the severity has been overridden.
True
if an error severity override has been set, False
otherwise.
|
inherited |
Python method signature(s):
printErrors(XMLErrorLog self, ostream stream=cerr) printErrors(XMLErrorLog self)
Prints all the errors or warnings stored in this error log.
This method prints the text to the stream given by the optional parameter stream
. If no stream is given, the method prints the output to the standard error stream.
The format of the output is:
N error(s): line NNN: (id) message
If no errors have occurred, i.e., getNumErrors() == 0
, then no output will be produced.
stream | the ostream or ostringstream object indicating where the output should be printed. |
def libsbml.SBMLErrorLog.remove | ( | self, | |
args | |||
) |
Python method signature(s):
remove(SBMLErrorLog self, long errorId)
Removes an error having errorId from the SBMLError list.
Only the first item will be removed if there are multiple errors with the given errorId.
errorId | the error identifier of the error to be removed. |
|
inherited |
Python method signature(s):
setSeverityOverride(XMLErrorLog self, long severity)
Set the severity override.
severity | an override code indicating what to do. If the value is LIBSBML_OVERRIDE_DISABLED (the default setting) all errors logged will be given the severity specified in their usual definition. If the value is LIBSBML_OVERRIDE_WARNING, then all errors will be logged as warnings. If the value is LIBSBML_OVERRIDE_DONT_LOG, no error will be logged, regardless of their severity. |
|
inherited |
Python method signature(s):
toString(XMLErrorLog self)string
Writes all errors contained in this log to a string and returns it.
This method uses printErrors() to format the diagnostic messages. Please consult that method for information about the organization of the messages in the string returned by this method.
|
inherited |
Python method signature(s):
unsetSeverityOverride(XMLErrorLog self)
Usets an existing override.